[gmx-users] mail reg diple moment fluctuation

Dear Justin    I want to study the filctuation of dipole moment near surface of CNT surrounded by water I want to peculiarly choose water molecules covering certain distance . how to choose such water molecules? With high regardsS.Vidhyasankar -- Gromacs Users mailing list *

[gmx-users] Mail reg g_energy tool

Dear justin  Thank you for your previous reply I  Need to extract various energy components at CNT-water interface is it possible to use .ndx file in g_energy tool otherwise How to study the energy of CNT-water interface. Thanks in advanceS.Visdhyasankar -- Gromacs Users mailing list * Please

[gmx-users] mail about g_dipoles

Dear Justin Thank you for your previous reply How To calculate fluctuation of dipole moment of water molecules   near (0.3nm)  the surface of CNT ,  Can i use  index.ndx  (ouput of g_select tool)  as input for g_dipoles? Thanks in advance -- Gromacs Users

[gmx-users] mail about g_select tool

Dear Justin thank you for your reply    I  wish to peculiarly select SOL  molecules within 0.7 nm from  the surface of CNT  to find dipole moment fluctuation  of those molecules . here i wish to choose g_select tool to get output index (-on)

[gmx-users] mail about contact angle

Dear Justin Thank you for your  previous help and reply , I have Effective interaction between (LJ short range) between CNT and Water .To further enlighten this May i use  contact  angle and Water density profile analysis? between CNT and water Or any other post processing tool available

[gmx-users] Mail regarding g_enemat tool

Dear justin Thank you for you reply Also when i use g_enemat tool as follows g_enemat_d -f CNTPEPRSOLIONSfulllatest3.edr -groups group.dat -emat jnnff.xpm it shows the following error Opened CNTPEPRSOLIONSfulllatest3.edr as single precision energy file Will read groupnames from inputfile Read

[gmx-users] mail about g_energy parameter

Dear justin thank you for your reply i used the following parameter in my mdp file cutoff-scheme= Group rlist= 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 rvdw

[gmx-users] About Analsysi tool

Dear Justin Thank you for your previous reply,      I am doing Dynamics for CNT-wraapped by Cyclic peptide .  The Cyclic peptide i am stacking Beyond Hydrogen bond distance.  AT end of Simulation, the Assembly become Collapsed

[gmx-users] mail About LJ obtained by g_energy

Dear Justin  Thank you for your previous reply    When i run the g_energy tool to find out  LJ-SR nad Lj-SR between  CYCLIPEPTIDE1  anf CNT it shows the negative value  -311.9    and   -2.45122     wha is the meaning of  this Negative Value?If LJ-SR LJ-LR then will

[gmx-users] Reg g_energy tool

Thank you justin  for your kind reply. As you told me in previous mail , the   g_energy  tool  is enough  to calculate interacton energy  (such as Coulombic and Vandeewaal's interaction , LJ interaction )  between groups  but How to choose two groups simulataneously in command prompt for

[gmx-users] About g_enemat tool

Dear Justin Thank you for your previous reply I want to calculate interaction energies (such as Coulombic and Vandeewaal's interaction , LJ interaction ) between groups    CNT and Cyclic peptide  for that I set energygrps = CNT  peptide1 petide2                     in mdp file When i extract 

[gmx-users] Regarding error in NPT SIMULATION in VACUM

Dear Justin Thank you for your previous reply When I run NPT equlibiriation for My CNT CNCASSED CYCLICPETIDE in VACUM I have Got the Following error after 3 lacs steps out of 10 lacs The X-size of the box (7.750338) times the

[gmx-users] (no subject)

Dear Justin Thank you for your previous reply When I run NPT equlibiriation for My CNT CNCASSED CYCLICPETIDE in VACUM I have Got the Following error after 3 lacs steps out of 10 lacs The X-size of the box (7.750338) times the

[gmx-users] Regarding Performance Tuning for GROMACS

Hai Justin Thank you for your Previous Reply Is there is Any Restrictions in usage of Number of Processor (in Clustering ) for Performance Tuning in gromacs 4 and After Version. especially when i use PME When I surf I got the Following Link

[gmx-users] About free enrgy calculation

Thank you for your previous reply Sorry  In previous Mail i wrongly  stated that decoupling CNT ( as you stated  it is big  Molecule ) To do free energy calculation based on on your tutorial 6( methane/water)   I  want to decouple  Water  from CNT which is Wrapped by  assembly of Cyclic

[gmx-users] Reg No error in output

Dear Justin Thank you for your Previous reply When i Run the Gromacs job in cluster the Job has been terminated withou any error . The md.log files does not show any error So i am not able to find out such abnormal termination . i have used the following script Should i remove the characrer 

[gmx-users] About Tutorials

Dear Justin Thank you For your previous reply   I would like to do REMD (Replica exchange MD) in gromacs I am very happy if you paste  tutorial for REMD, Targeted MD , Constraint MD  and Non Equilibrium MD   as

[gmx-users] Reg Replica exchange Molecular dynamics

Dear Justin Thank you For your previous reply   I would like to do REMD (Replica exchange MD) in gromacs I am very happy if you paste  tutorial for REMD, Targeted MD , Constraint MD  and Non Equilibrium MD  as

[gmx-users] About free energy Methods for Memebrane-protein Calculation

Dear Justin ,   Thank you for your Previous reply. I am Doing Simulation of assembly of  Cyclic Petide in POPC membrane For that I need to calculate Free energy for Stability of Assembly. Normally Membrane Tutorail Does not contain Free Energy Calculation. So which Method is